[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

[SAPNA BORAH]

hi
Thanks for the suggestion. I will give this a shot, and remove these
restraints.

I am unclear about what should I be looking in the log file as you
mentioned. The conformations are not just close, they are the same as the
initial conformation.

I have some understanding on pbc that serves a problem in visualisation of
the trajectory. I have applied the all sorts of pbc options, but somehow
things are not falling into place.

However the problem more grave here, for me, is the production run and the
model stability that is happening throughout the simulations in different
versions.


Thanks.
Sapna

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Mon, Feb 29, 2016 at 11:59 AM, Dries Van Rompaey <
dries.vanrompaey at gmail.com> wrote:

> Hi,
> Looks like you might be applying positional restraints (define =-DPOSRES in
> your mdp file). This is standard practice for equilibration, but I don't
> think you want to be doing this for your production run, as this will
> restrain your protein to conformations rather close to your starting
> conformation. Check if this is the case in your logfile.
>
> Proteins coming 'out of the box' is caused by periodic boundary conditions.
> This is probably not a problem. Read this for more information:
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> Sometimes one pass of trjconv isn't enough to sort everything out and more
> might be needed.
>
> Kind regards
>
> Dries
> On 29 Feb 2016 5:25 a.m., "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:
>
> > Dear Mark,
> >
> > I have still not been able to solve my problem. A whole new problem has
> now
> > arisen. I am listing them as follows:
> >
> > 1. I am running 100ns simulations for 6 protein models and I was using
> both
> > version 4.6.5 and 5.0.4 when I found that after production run, my
> protein
> > models are behaving differently in both the versions. I am attaching the
> > images of rmsd differences in the link attached. Also, find the mdp files
> > attached used in both the versions.
> >
> > 2. I have run multiple runs for the models to see if there are changes,
> but
> > everytime, each of the models is very very stable and does not change in
> > conformation at all in 5.0.4 but does otherwise in 4.6.5.
> >
> > 3. There is another problem that the protein comes out of the water box
> in
> > 4.6.5 and not in 5.0.4 in all the simulations. I have ensured to remove
> > jumps from the trajectories, make molecules whole.
> >
> > Please help me in this regard.
> >
> > http://dropcanvas.com/v0k0b
> >
> > Regards,
> > Sapna.
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> >
> > On Thu, Feb 11, 2016 at 10:54 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Sapna,
> > >
> > > The list doesn't allow attachments. Please put them somewhere online
> and
> > > provide a link.
> > > The differences can be large. Can't tell if you don't know the possible
> > > range of conformations/trajectories for one Gromacs version.
> > > Did you ensure to remove jumps from the trajectories and/or make
> > molecules
> > > whole, etc? That would be the only thing we'd be able to see from the
> > RMSD
> > > plot anyway, whether you removed jumps or not. Otherwise it does not
> > > contain useful information (in this regard).
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On Feb 11, 2016 05:28, "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:
> > >
> > > > Dear Mark,
> > > >
> > > > Please find attached a plot showing the RMSD difference. It is for
> the
> > > same
> > > > protein.
> > > >
> > > > Even if the same runs are not reproducible, my doubt is whether there
> > can
> > > > be such a large variation in the RMSD trend. Which data should I rely
> > on
> > > > then, it is giving me a hard time.
> > > >
> > > > I'll be grateful if you look into this.
> > > >
> > > > Thanks,
> > > > Sapna.
> > > >
> > > > Sapna Mayuri Borah
> > > > c/o Dr. A. N. Jha
> > > > Research student
> > > > Tezpur University,
> > > > India
> > > >
> > > > On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham <
> mark.j.abraham at gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > This is quite normal.
> > > > > http://www.gromacs.org/Documentation/Terminology/Reproducibility.
> > You
> > > > > should see a similar range of variation in the trajectories
> produced
> > in
> > > > the
> > > > > two versions that are incompletely sampling the same ensemble, but
> > one
> > > > can
> > > > > say very little about two single observed trajectories sampled from
> > > them.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH <sapnauser365 at gmail.com
> >
> > > > wrote:
> > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > I have tried running the same protein in the two versions of
> > gromacs
> > > > > 4.6.5
> > > > > > and 5.0.4. Now, both the runs are producing entirely different
> > > results.
> > > > > >
> > > > > > The results till equilibration are same.
> > > > > >
> > > > > > After the run however, there is a total change in the production
> > > > > results. I
> > > > > > have used the same mdp files.
> > > > > >
> > > > > > I have rerun the systems and they still produce similar results
> in
> > > the
> > > > > same
> > > > > > version.
> > > > > >
> > > > > > The protein structure is a modelled one.
> > > > > >
> > > > > >
> > > > > > Thanks in advance.
> > > > > > Sapna.
> > > > > >
> > > > > > Sapna Mayuri Borah
> > > > > > c/o Dr. A. N. Jha
> > > > > > Research student
> > > > > > Tezpur University,
> > > > > > India
> > > > > > --
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